|Genomic Dark Matter Infected With Ancient Viral DNA|
|SciMed - Genetics & Genome|
|TS-Si News Service|
|Wednesday, 25 April 2012 08:00|
New York, NY, USA. Ninety percent of every mammal's genome is dark matter harboring ancient viral DNA that infected our ancestors from as far back as the age of the dinosaurs.
Scientists have uncovered clues as to how our genomes became riddled with viruses, revealing important new information.
Scientists have struggled for years with the observation that more than 90 percent of every mammal's genome has no known function. Finding that mammals host ancient virus material in such abundant quantities, researchers at Oxford University, the Aaron Diamond AIDS Research Center (New York), and the Rega Institute (Belgium) set out to understand how so much of this ancient viral materials got into their hosts' genomes in the first place. Their findings appear in the journal Proceedings of the National Academy of Sciences (PNAS).
The research team searched the genomes of 38 mammals covering a large range of species: from mouse, rat and bat to human, elephant and dolphin.
Genetic material from all of the residing viruses was collected and then compared using mathematical models.One particular group of viruses had lost the ability to infect new cells. Their genetic material is still able to amplify itself but the whole lifecycle of the virus is passed within a single cell. This change, they found, was followed by a dramatic proliferation of the virus' genetic material within the genomes.
A comparison with all of the other viruses in the genomes revealed this to be a universal phenomenon, and that loss of cell infectivity is associated with a roughly 30-fold increase in the abundance of the virus.
Gkikas Magiorkinis from Oxford University's Zoology Department, and the lead author, says "We know that much of the dark matter in our genome plays by its own rules, in the same way as an epidemic in an infectious disease, but operating over millions of years."
During epidemic outbreaks, a relatively small proportion of infected people are often responsible for most of the spread of an infectious agent to the rest of the population. They are described as superspreaders.
Robert Belshaw from the same Oxford department, who led the study, suspects that these viruses are forced to make a choice: either to keep their viral essence and spread between animals and species, or to commit to one genome and then spread massively within it. "This is the story of the epidemic within every animal's genome, a story which has been going on for 100 million years and which continues today."
FundingThe study was supported by the Wellcome Trust.
CitationEnv-less endogenous retroviruses are genomic superspreaders. Gkikas Magiorkinis, Robert J. Gifford, Aris Katzourakis, Joris De Ranter, and Robert Belshaw. Proceedings of the National Academy of Sciences 2012. doi:10.1073/pnas.1200913109
Includes Supporting Information
Endogenous retroviruses (ERVs) differ from typical retroviruses in being inherited through the host germline and therefore are a unique combination of pathogen and selfish genetic element. Some ERV lineages proliferate by infecting germline cells, as do typical retroviruses, whereas others lack the env gene required for virions to enter cells and thus behave like retrotransposons. We wished to know what factors determined the relative abundance of different ERV lineages, so we analyzed ERV loci recovered from 38 mammal genomes by in silico screening. By modeling the relationship between proliferation and replication mechanism in detail within one group, the intracisternal A-type particles (IAPs), and performing simple correlations across all ERV lineages, we show that when ERVs lose the env gene their proliferation within that genome is boosted by a factor of ~30. We also show that ERV abundance follows the Pareto principle or 20/80 rule, with ~20% of lineages containing 80% of the loci. This rule is observed in many biological systems, including infectious disease epidemics, where commonly ~20% of the infected individuals are responsible for 80% of onward infection. We thus borrow simple epidemiological and ecological models and show that retrotransposition and loss of env is the trait that leads endogenous retroviruses to becoming genomic superspreaders that take over a significant proportion of their host's genome.
|Last Updated on Wednesday, 25 April 2012 08:05|